free software and bioinformatics
DESCRIPTION
an overview of the free software philosophy as it has been applied on the bioinformatics fieldTRANSCRIPT
![Page 2: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/2.jpg)
When Craig Venterwas asked, “Whatmakes you think youcan do a better jobwith life and geneticsthan God?”, he answered…
![Page 3: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/3.jpg)
we have computers
![Page 4: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/4.jpg)
and software too
![Page 5: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/5.jpg)
¡free software!
![Page 6: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/6.jpg)
biology is a data intensive science
![Page 7: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/7.jpg)
![Page 8: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/8.jpg)
Scientificinformationavailable in 2010 will double every72 hours
![Page 9: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/9.jpg)
![Page 10: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/10.jpg)
data mining
![Page 11: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/11.jpg)
my data is mine!
![Page 12: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/12.jpg)
and your data is mine, too!
![Page 13: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/13.jpg)
open sourceopen dataopen access
![Page 14: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/14.jpg)
open science
![Page 15: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/15.jpg)
Comparative genomicsSequence (DNA/RNA)
& phylogeny
Regulation of gene expression; transcription factors & micro RNAs
Protein sequence analysis &evolution
Protein families, motifs and domains
Protein structure & function: computational crystallography
Protein interactions & complexes: modelling and prediction
Chemical biology
Pathway analysis
Systems modelling
Image analysis
Data integration & literature mining
![Page 16: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/16.jpg)
The first Atlas of Protein Sequence and Structure, presented information about 65 proteins.
![Page 17: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/17.jpg)
In 1981 the EMBL Nucleotide Sequence Data Library is created. Version 2 was composed of 811 secuences, around 1 millionbases introduced by hand.
![Page 18: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/18.jpg)
Smith TF, Waterman MS (1981). "Identification of common molecular subsequences.". J Mol Biol. 147 (1): 195‐7.
![Page 19: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/19.jpg)
S.F. Altschul, et al. (1990), "Basic Local Alignment Search Tool," J. Molec. Biol., 215(3): 403‐10, 1990. 15,306 citations
![Page 20: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/20.jpg)
J. Thompson, T. Gibson, D. Higgins (1994), CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment. Nuc. Acids. Res. 22, 4673 ‐ 4680
![Page 21: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/21.jpg)
In 1995 the European bioinformatics institute is created.
![Page 22: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/22.jpg)
EMBOSS (The European Molecular Biology Open Software Suite) is a free Open Source software analysis package that provides a comprehensive set of sequence analysis package specially developed for the needs of the molecular biology user community.
First requirements based on a list of long‐standing problems in existing commercial software (GCG), and the need for public source code
Within EMBOSS you will find around 200 programs (applications).
Current version is 6.0.1
http://emboss.sourceforge.net/
![Page 23: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/23.jpg)
Main Programs in EMBOSS
Retrieve sequences from databaseSequence alignmentNucleic gene finding and translationProtein secondary structure predictionRapid database searching with sequence patternsProtein motif identification, including domain analysisNucleotide sequence pattern analysis, for example to identify CpG islands or repeats.Codon usage analysis for small genomesRapid identification of sequence patterns in large scale sequence setsPresentation tools for publication
![Page 24: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/24.jpg)
![Page 25: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/25.jpg)
open‐bio.org
• The Open Bioinformatics Foundation is a non profit, volunteer run organization focused on supporting open source programming in bioinformatics.
• Its main activities are:– Underwriting and supporting the BOSC conferences
– Organizing and supporting developer‐centric "hackathon" events (Bio*)
2
![Page 26: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/26.jpg)
![Page 27: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/27.jpg)
O’Reilly Books and Conferences
![Page 28: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/28.jpg)
![Page 29: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/29.jpg)
http://www.ensembl.org
![Page 30: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/30.jpg)
30http://www.uniprot.org
![Page 31: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/31.jpg)
GenericModel Organism Database projecthttp://gmod.org
![Page 32: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/32.jpg)
DAS Concept
Reference server
Annotation server BAnnotation server A Annotation server C
Clienthttp://www.biodas.org
![Page 33: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/33.jpg)
DAS Server
• DAS request to retrieve features on a segment:
• http://das.ensembl.org/das/ens_36_omim_genes/features?segment=1:1,1000000
• Result:
![Page 34: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/34.jpg)
Das viewer
![Page 35: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/35.jpg)
http://www.ebi.ac.uk/dasty/
![Page 36: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/36.jpg)
Applied Biosystems ABI 3730XL
Illumina / Solexa Genetic Analyzer
Applied BiosystemsSOLiD
Roche / 454 Genome Sequencer
1 Mb/day 100 Mb/run 3000 Mb/run
![Page 37: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/37.jpg)
Sequencing Fragment assembly problem The Shortest Superstring Problem Velvet (Zerbino, 2008)
Gene finding Hidden Markov Models, pattern recognition methods GenScan (Burge & Karlin, 1997)
Sequence comparison pairwise and multiple sequence alignments dynamic algorithm, heuristic methods PSI‐ BLAST (Altschul et. al., 1997) (SSAHA, 2001) (MUMmerGPU, 2008)
![Page 38: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/38.jpg)
![Page 39: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/39.jpg)
Genomes
Nucleotides
Proteins
Structures
Other molecules
Interactions
Experiments
Literature
Ontologies
http://www.ebi.ac.uk/Databases/
![Page 40: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/40.jpg)
Curso práctico de base de datos e integración de información biológica
![Page 41: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/41.jpg)
Challenges of Data Integration
• Different types of data (sequence, function, literature etc.)
• Different data formats (FASTA, EMBL, Genbank, tab delimited etc.)
• Different storage formats (ASCII flatfile, XML, RDBMS)
• No standard formats for common fields (citations, descriptions, dates etc.)
• Volume and size of data
![Page 42: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/42.jpg)
BioMart is a simple and robust data integration system for large scale data querying, providing researchers with fast and flexible access to biological databases
http://www.biomart.org/
![Page 43: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/43.jpg)
Web Services
http://www.ebi.ac.uk/Tools/
![Page 44: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/44.jpg)
Challenges when using tools in unison
• Manually transfer data from one application to another
• Understand disparate data formats
• Convert file formats where appropriate
• Manage and understand disparate application environments e.g. web browser, desktop application
![Page 45: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/45.jpg)
![Page 46: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/46.jpg)
dataflow workflow
ws ws ws ws ws
curation
submission
![Page 47: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/47.jpg)
REST: REpresentational State Transfer
http://www.ebi.ac.uk/Tools/webservices/rest/dbfetch/uniprot/slpi_human
GET, POST
HTML,XML,PNG
RESTful web services
![Page 48: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/48.jpg)
Any web page is a web servicehttp://www.ebi.ac.uk/cgi-bin/dbfetch?db=uniprot&id=alk1_human&style=html&format=default
![Page 49: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/49.jpg)
Friendly URL and XML documents
• http://www.ebi.ac.uk/Tools/webservices/rest/dbfetch/uniprot/slpi_human
• http://www.ebi.ac.uk/Tools/webservices/rest/dbfecth/uniprot/slpi_human/xml
• http://www.ebi.ac.uk/Tools/webservices/rest/dbfetch/uniprot/slpi_human/fasta
![Page 50: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/50.jpg)
Biomart query
<Query virtualSchemaName="central_server_1"><Dataset name="hsapiens_gene_ensembl" >
<Attribute name="ensembl_gene_id"/><Attribute name="ensembl_transcript_id"/><Filter name="chromosome_name" value="1"/><Filter name="band_end" value=”p36.33"/><Filter name="band_start" value=”q44"/>
</Dataset><Dataset name="msd">
<Attribute name="pdb_id"/><Attribute name=”experiment_type"/><Filter name="experiment_type" value=”NMR"/>
</Dataset></Query>
![Page 51: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/51.jpg)
SOAP: Simple Object Access ProtocolfetchData(uniprot,wap_rat,default,xml)
SOAP services
![Page 52: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/52.jpg)
fetchData (db, id, format, style)
entry
wsdbfetch
![Page 53: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/53.jpg)
Perl client
use SOAP::Lite;
my $WSDL='http://www.ebi.ac.uk/Tools/webservices/wsdl/WSDbfetch.wsdl'; my $soap = SOAP::Lite->service($WSDL);
# fetchData dbName:id <format> <style>
my $result = $soap->fetchData(‘uniprot’, ‘default’, ‘raw’); die $soap->call->faultstring if $soap->call->fault;
foreach my $i (@$result) { print "$i\n"; }
![Page 54: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/54.jpg)
EBI web services (analysis tools)
jobid
getResults (jobid)
results available
checkStatus (jobid)
status
run(params, data)
poll (jobid, type)
result file
![Page 55: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/55.jpg)
use SOAP::Lite;
my $WSDL = 'http://www.ebi.ac.uk/Tools/webservices/wsdl/WSFasta.wsdl'; my $fasta_client = SOAP::Lite->service($WSDL);
my %params=(); $params{'program'}='fasta3'; $params{'database'}='uniprot';$params{'email'}='[email protected]';$params{‘async'}= 1;
$data={type=>"sequence",content=>"MRCSISLVLGLLALEVALARNLQEHVFNSVQSMCSDDSFSEDTECI"};
# $data={type=>"sequence",# content=>“uniprot:slpi_human"};
my $jobid = $fasta_client >runFasta(SOAP::Data->name('params')->type(map=>\%params), SOAP::Data->name( content => [$data]));
print $fasta_client->poll($jobid);
Perl client
![Page 56: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/56.jpg)
Perl client (cont.)# set a loop for checking job submission status # RUNNING, NOT_FOUND, ERROR, DONE
my $status = $fasta_client ->checkStatus($jobid); while (status eq "RUNNING") {sleep 10; $status = $fasta_client->checkStatus($jobid); }
# when job is done, poll for the results
my $result = $fasta_client ->poll($jobid) if ($status eq "DONE") ;
print $result;
![Page 57: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/57.jpg)
http://taverna.sourceforge.net/
![Page 58: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/58.jpg)
http://www.myexperiment.org/users/471
![Page 59: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/59.jpg)
![Page 60: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/60.jpg)
high throughput genomics
![Page 61: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/61.jpg)
data management
![Page 62: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/62.jpg)
https://carmaweb.genome.tugraz.at/
http://base.thep.lu.se/
![Page 63: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/63.jpg)
Why must support standards?
• Unambiguous representation, description and communication– Final results and metadata
• Interoperability – Data management and analysis
• Integration of OMICS system biology
![Page 64: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/64.jpg)
What to standarize?
• CONTENT: Minimal/Core Information to be reported ‐> MIBBI (http://www.mibbi.org)
• SEMANTIC: Terminology Used ‐> Ontologies, OBI (http://obi‐ontology.org)
• SYNTAX: Data Model, Data Exchange ‐>Fuge (http://fuge.sourceforge.net/) ISA‐TAB, MAGE‐TAB, PRIDE
![Page 65: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/65.jpg)
MIBBI: Standard Content
Promoting Coherent Minimum Reporting Requirements for Biological and Biomedical Investigations: The MIBBI Project, Taylor et Al, Nature Biotechnology
![Page 66: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/66.jpg)
data analysis
![Page 67: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/67.jpg)
Microarray
RT‐PCR
Biological question
Testing
Biological verification and interpretation
Microarray experiment
Estimation
Experimental design
Image analysis
Normalization
Clustering Prediction
Expression quantification Pre‐processing
Analysis
![Page 68: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/68.jpg)
r‐project.org
• R is an open source implementation of the S Language • Many statistical and machine learning algorithms• Good visualization capabilities• Possible to write scripts that can be reused• Sophisticated package creation and distribution system• Supports many data technologies: XML, DBI, SOAP• Interacts with other languages: C; Perl; Python; Java• R is largely platform independent: Unix; Windows; OSX• R has an active user community
cran.r‐project.org
![Page 69: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/69.jpg)
BioConductor
• Access wide range of powerful statistical and graphical tools• Facilitate the integration of biological metadata in the analysis of
experimental data• Allow the rapid development of extensible, scalable, and
interoperable software; • Promote high‐quality documentation and reproducible research.• Provide training in computational and statistical methods for the
analysis of genomic data.
http://www.bioconductor.org/
![Page 70: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/70.jpg)
Bioconductor Packages/libraries
Two releases each year that follow the biannual releases of R
294 software packages
490 Metadata packages
>700 citations
Release 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 2.0 2.1 2.2 2.3 ‐> 294 packages
No. softw
are packages
![Page 71: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/71.jpg)
Bioconductor for Microarray Analysis
• Quickly becoming the accepted approach
• Open source
• Flexible
• (fairly) simple to use ‐ intuitive
• Wide applications – many packages
![Page 72: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/72.jpg)
affy packagePre-processing oligonucleotide chip data:• diagnostic plots, • background correction, • probe-level normalization,• computation of expression measures.
imageplotDensity
plotAffyRNADeg
barplot.ProbeSet
![Page 73: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/73.jpg)
heatmap
mva package
![Page 74: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/74.jpg)
![Page 75: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/75.jpg)
proteomics
![Page 76: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/76.jpg)
http://www.agml.org/
![Page 77: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/77.jpg)
Trans‐Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics
http://tools.proteomecenter.orghttp://proteowizard.sourceforge.nethttp://www.thegpm.org/TANDEM
![Page 78: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/78.jpg)
Bioclipse
View
View
Editor
ConsoleProperties
http://www.bioclipse.net/
![Page 79: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/79.jpg)
Work with spectra: Spectrum plugin
![Page 80: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/80.jpg)
Work with sequences: BioJava plugin
![Page 81: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/81.jpg)
CMLRSS plugin: Chemistry on the web
![Page 82: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/82.jpg)
cytoscape
http://www.cytoscape.org
![Page 83: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/83.jpg)
pyMol
http://www.pymol.org
![Page 84: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/84.jpg)
image processing
![Page 85: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/85.jpg)
Open Microscopy Environment
• OME is a multi‐site collaborative effort among academic laboratories and a number of commercial entities that produces open tools to support data management for biological light microscopy.
• The original OME server is an application written in Perl running under Apache. It is accessed using a Web User Interface, via a Java API, or using a plugin for ImageJ.
• The server can support images in a wide range of file formats. This model is also extendable allowing custom data to be stored in the server.
• It supports multiple users and provides appropriate security for private research and collaboration.
http://openmicroscopy.org
![Page 86: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/86.jpg)
OMERO
![Page 87: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/87.jpg)
![Page 88: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/88.jpg)
OMERO
![Page 89: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/89.jpg)
beyond software
![Page 90: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/90.jpg)
At $150,000, the Polonator is the cheapestinstrument on the market, says Harvard University's George Church, whose labdeveloped the technology in conjunctionwith Dover Systems, Plus, the tool uses five‐fold less reagents than other platforms, and is the smallest instrument available.
http://www.polonator.org/
![Page 91: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/91.jpg)
http://www.igem.org
http://www.bioparts.org/
![Page 92: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/92.jpg)
where is the stuff
![Page 93: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/93.jpg)
http://bioinformatics.oxfordjournals.org
![Page 94: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/94.jpg)
http://nar.oxfordjournals.org
![Page 95: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/95.jpg)
http://www.biomedcentral.com/bmcbioinformatics/
![Page 96: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/96.jpg)
http://genomebiology.com/software/
![Page 97: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/97.jpg)
the future
![Page 98: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/98.jpg)
Growth of open access scientistsdigital natives, always online, hybrids
catalysts for change
[Phil Bourne]
![Page 99: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/99.jpg)
![Page 100: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/100.jpg)
• Making scientific research “re‐useful”—We help people and organizations open and mark their research and data for reuse.
• Enabling “one‐click” access to research materials—We help streamline the materials‐transfer process so researchers can easily replicate, verify and extend research.
• Integrating fragmented information sources—We help researchers find, analyze and use data from disparate sources by marking and integrating the information with a common, computer‐readable language.
![Page 101: Free software and bioinformatics](https://reader033.vdocuments.net/reader033/viewer/2022052904/55832173d8b42a6e768b4d6b/html5/thumbnails/101.jpg)